Mercurial > repos > tduigou > icfree_calibrator

comparison calibrator.xml @ 3:c5cd3420fed6 draft default tip

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 8dde46bddbe8df819c48e7e392893c34b22aa6dd
author tduigou
date Fri, 20 Dec 2024 09:32:09 +0000
parents ac296a9146df
children
comparison
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2:ac296a9146df 3:c5cd3420fed6
30 #end if 30 #end if
31 #if str($adv.num_samples) != '' 31 #if str($adv.num_samples) != ''
32 --num '$adv.num_samples' 32 --num '$adv.num_samples'
33 #end if 33 #end if
34 'extractor.csv' 'reference.csv' && 34 'extractor.csv' 'reference.csv' &&
35 mv 'calibrated.csv' '$output_calibrated' 35 mv 'calibrated.csv' '$output_calibrated' &&
36 mv 'calibrated_control_points.csv' '$output_control_points'
36 ]]></command> 37 ]]></command>
37 <inputs> 38 <inputs>
38 <param name="initial_data_file" type="data" format="csv" label="Initial file" help="Initial file"/> 39 <param name="initial_data_file" type="data" format="csv" label="Initial file" help="Initial file"/>
39 <param name="sampling_file" type="data" format="csv" label="Sampling file" help="Sampling file"/> 40 <param name="sampling_file" type="data" format="csv" label="Sampling file" help="Sampling file"/>
40 <param name="ref_file" type="data" format="csv" label="Reference input file" help="Reference input file"/> 41 <param name="ref_file" type="data" format="csv" label="Reference input file" help="Reference input file"/>
49 <param argument="num_control_points" type="integer" optional="true" label="Number of control points to select" help="Number of control points to select" /> 50 <param argument="num_control_points" type="integer" optional="true" label="Number of control points to select" help="Number of control points to select" />
50 </section> 51 </section>
51 </inputs> 52 </inputs>
52 <outputs> 53 <outputs>
53 <data name="output_calibrated" format="csv" label="${tool.name} - Calibrated yields" /> 54 <data name="output_calibrated" format="csv" label="${tool.name} - Calibrated yields" />
55 <data name="output_control_points" format="csv" label="${tool.name} - Control points" />
54 <data name="output_graph" format="png" label="${tool.name} - Graph" /> 56 <data name="output_graph" format="png" label="${tool.name} - Graph" />
55 </outputs> 57 </outputs>
56 <tests> 58 <tests>
57 <test expect_num_outputs="2"> 59 <test expect_num_outputs="3">
58 <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.csv -output_file calibrator.extractor_output.1.csv --> 60 <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.csv -output_file calibrator.extractor_output.1.csv -->
59 <!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.1.csv -jove_plus 3 -jove_minus 2 -plot calibrator.output.1.png calibrator.output.extractor.1.csv calibrator.input.ref.csv --> 61 <!-- python -m icfree.learner.calibrator -output calibrator.output.calibrated.1.csv -jove_plus 3 -jove_minus 2 -plot calibrator.output.1.png calibrator.output.extractor.1.csv calibrator.input.ref.csv -->
60 <param name="initial_data_file" value="calibrator.input.initial_data.csv" /> 62 <param name="initial_data_file" value="calibrator.input.initial_data.csv" />
61 <param name="sampling_file" value="calibrator.input.sampling.csv" /> 63 <param name="sampling_file" value="calibrator.input.sampling.csv" />
62 <param name="ref_file" value="calibrator.input.ref.csv" /> 64 <param name="ref_file" value="calibrator.input.ref.csv" />
65 <output name="output_calibrated" ftype="csv"> 67 <output name="output_calibrated" ftype="csv">
66 <assert_contents> 68 <assert_contents>
67 <has_n_lines n="58" /> 69 <has_n_lines n="58" />
68 </assert_contents> 70 </assert_contents>
69 </output> 71 </output>
72 <output name="output_control_points" ftype="csv">
73 <assert_contents>
74 <has_n_lines n="6" />
75 </assert_contents>
76 </output>
70 <output name="output_graph" ftype="png" > 77 <output name="output_graph" ftype="png" >
71 <assert_contents> 78 <assert_contents>
72 <has_size value="45000" delta="2000" /> 79 <has_size value="45000" delta="2000" />
73 </assert_contents> 80 </assert_contents>
74 </output> 81 </output>
75 </test> 82 </test>
76 <test expect_num_outputs="2"> 83 <test expect_num_outputs="3">
77 <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.tsv -output_file calibrator.output.extractor.2.csv -num_samples 20 -num_replicates 3 --> 84 <!-- python -m icfree.learner.extractor -initial_data_file calibrator.input.initial_data.csv -sampling_file calibrator.input.sampling.tsv -output_file calibrator.output.extractor.2.csv -num_samples 20 -num_replicates 3 -->
78 <!-- python -m icfree.learner.calibrator -plot calibrator.output.2.png -output calibrator.output.2.csv -jove_plus 4 -jove_minus 3 -r2_limit 0.9 -num 20 -num_control_points 4 calibrator.output.extractor.2.csv calibrator.input.ref.csv --> 85 <!-- python -m icfree.learner.calibrator -plot calibrator.output.2.png -output calibrator.output.2.csv -jove_plus 4 -jove_minus 3 -r2_limit 0.9 -num 20 -num_control_points 4 calibrator.output.extractor.2.csv calibrator.input.ref.csv -->
79 <param name="initial_data_file" value="calibrator.input.initial_data.csv" /> 86 <param name="initial_data_file" value="calibrator.input.initial_data.csv" />
80 <param name="sampling_file" value="calibrator.input.sampling.csv" /> 87 <param name="sampling_file" value="calibrator.input.sampling.csv" />
81 <param name="ref_file" value="calibrator.input.ref.csv" /> 88 <param name="ref_file" value="calibrator.input.ref.csv" />
88 <output name="output_calibrated" ftype="csv"> 95 <output name="output_calibrated" ftype="csv">
89 <assert_contents> 96 <assert_contents>
90 <has_n_lines n="21" /> 97 <has_n_lines n="21" />
91 </assert_contents> 98 </assert_contents>
92 </output> 99 </output>
100 <output name="output_control_points" ftype="csv">
101 <assert_contents>
102 <has_n_lines n="21" />
103 </assert_contents>
104 </output>
93 <output name="output_graph" ftype="png" > 105 <output name="output_graph" ftype="png" >
94 <assert_contents> 106 <assert_contents>
95 <has_size value="38000" delta="1000" /> 107 <has_size value="38000" delta="1000" />
96 </assert_contents> 108 </assert_contents>
97 </output> 109 </output>
98
99 </test> 110 </test>
100
101 </tests> 111 </tests>
102 <help><![CDATA[ 112 <help><![CDATA[
103 Calibrator 113 Calibrator
104 ========== 114 ==========
105 Calculate yield based on fluorescence data and apply calibration. 115 Calculate yield based on fluorescence data and apply calibration.